ArticleBiology methods & protocols2022
PSSMCOOL: a comprehensive R package for generating evolutionary-based descriptors of protein sequences from PSSM profiles.
Article in Biology methods & protocols, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- Integrating evolutionary and compositional features with ML and DL for robust and interpretable druggable protein prediction.Journal of computer-aided molecular design · 2026Article
- ProtDML: label-aware representation learning for broad-spectrum protein function prediction.Briefings in bioinformatics · 2026Article
- DDGWizard: Integration of feature calculation resources for analysis and prediction of changes in protein thermostability upon point mutations.PLoS computational biology · 2025Article
- A deep learning framework for lysine 2-hydroxyisobutyrylation site prediction using evolutionary feature representation.Scientific reports · 2025Article
- SARST2 high-throughput and resource-efficient protein structure alignment against massive databases.Nature communications · 2025Article
- Multimodal deep learning for allergenic proteins prediction.BMC biology · 2025Article
- Article
- Bacteriocin prediction through cross-validation-based and hypergraph-based feature evaluation approaches.Frontiers in bioinformatics · 2025Article
- PON-Tm: A Sequence-Based Method for Prediction of Missense Mutation Effects on Protein Thermal Stability Changes.International journal of molecular sciences · 2024Article
- ProkDBP: Toward more precise identification of prokaryotic DNA binding proteins.Protein science : a publication of the Protein Society · 2024Article
- EnsembleDL-ATG: Identifying autophagy proteins by integrating their sequence and evolutionary information using an ensemble deep learning framework.Computational and structural biotechnology journal · 2023Article
- BPAGS: a web application for bacteriocin prediction via feature evaluation using alternating decision tree, genetic algorithm, and linear support vector classifier.Frontiers in bioinformatics · 2023Article
- Generation of Optimized Consensus Sequences for Hepatitis C virus (HCV) Envelope 2 Glycoprotein (E2) by a Modified Algorithm: Implication for a Pan-genomic HCV Vaccine.Avicenna journal of medical biotechnologyArticle
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5 authors.
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Abstract
Position-specific scoring matrix (PSSM), also called profile, is broadly used for representing the evolutionary history of a given protein sequence. Several investigations reported that the PSSM-based feature descriptors can improve the prediction of various protein attributes such as interaction, function, subcellular localization, secondary structure, disorder regions, and accessible surface area. While plenty of algorithms have been suggested for extracting evolutionary features from PSSM in recent years, there is not any integrated standalone tool for providing these descriptors. Here, we introduce PSSMCOOL, a flexible comprehensive R package that generates 38 PSSM-based feature vectors. To our best knowledge, PSSMCOOL is the first PSSM-based feature extraction tool implemented in R. With the growing demand for exploiting machine-learning algorithms in computational biology, this package would be a practical tool for machine-learning predictions.
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